Re: [gmx-users] Segmentation Fault (Address not mapped)

darre...@ece.ubc.ca wrote: Dear GROMACS Gurus, I am experiencing a segmentation fault when mdrun executes. My simulation has a graphene lattice with an array (layer) of ammonia molecules above it. The box is three times the width of the graphene lattice, three times the length of the graphene lat

[gmx-users] Segmentation Fault (Address not mapped)

Dear GROMACS Gurus, I am experiencing a segmentation fault when mdrun executes. My simulation has a graphene lattice with an array (layer) of ammonia molecules above it. The box is three times the width of the graphene lattice, three times the length of the graphene lattice, and three times the he

[gmx-users] Re: GMX-Installation2

On Wed, 2009-07-01 at 22:44 -0700, nanogr...@ymail.com wrote: > Dear Jussi, > > Hi, > > Thanks for your help, > > Because of some problems with fedora 10, I installed Fedora 11. If you installed the rpms included in Fedora as I told before, there's one more thing you should know (which is do

[gmx-users] Problems with non-bonded interactions using OPLSAA

Dear all I would like to simulate beta cyclodextrin in various organic solvents with the OPLSAA FF for Carbohydrates (J Comput Chem 18: 1955-1970, 1997) but am having problems with the short range Coulomb and LJ interactions. This FF (and OPLS in general) does not assign LJ parameters to hydrogen

[gmx-users] False C6/C12 parameter for DMSO and chloroform in GROMOS 45a3 force field (ffG45a3)

Dear gmx-users (and developers ;-) I believe there are false LJ pair-parameters in gromacs' implementation of the GROMOS 45a3 force field for interactions between the atoms of DMSO, and between the atoms of chloroform. The C6/C12 pair paramteters for CDMSO-SDMSO, ODMSO-SDMSO, ODMSO-CDMSO, and CLCH

Re: [gmx-users] problem in g_order

Dear Erik, oo.i will be more meticulous next time. It works. :) thanks again. Regards, bing On Thu, Jul 2, 2009 at 9:38 PM, Erik Marklund wrote: > I see one typo. See below. > > Bing Bing skrev: > >> Dear all, >> I had created 3-21 group of sn1 chain for order analysis. I have issued:- >> >

Re: [gmx-users] problem in g_order

I see one typo. See below. Bing Bing skrev: Dear all, I had created 3-21 group of sn1 chain for order analysis. I have issued:- make_ndx_d -f md_0_1.tpr -o sn1.dx Here's the typo. You probably have an index file named sn1.dx.ndx > a C15 Found 128 atoms with name C15 3 C15

[gmx-users] problem in g_order

Dear all, I had created 3-21 group of sn1 chain for order analysis. I have issued:- make_ndx_d -f md_0_1.tpr -o sn1.dx > a C15 Found 128 atoms with name C15 3 C15 : 128 atoms > a C16 Found 0 atoms with name C16 Group is empty > a C17 Found 128 atoms with name C17 4 C1

Re: [gmx-users] problem in energy minimisation of dna-protein complex

nitu sharma wrote: Dear all I am doing simulation of dna -protein complex . in this processing I am getting error in energy minimisation step- the error comes like this- There were 2 inconsistent shifts. Check your topology There were 4 inconsistent shifts. Check your topolo

[gmx-users] problem in energy minimisation of dna-protein complex

Dear all I am doing simulation of dna -protein complex . in this processing I am getting error in energy minimisation step- the error comes like this- There were 2 inconsistent shifts. Check your topology There were 4 inconsistent shifts. Check your topology Steepest Descents:

Re: [gmx-users] broken protein

P.R.Anand Narayanan wrote: Dear users, How will I be able to run a simulation on a protein with 2chains if it is broken. I heard that the protein might have been broken which was observed from the failure of energy minimization which ended in just 1 step. "Broken" is a very generic term f

[gmx-users] broken protein

Dear users, How will I be able to run a simulation on a protein with 2chains if it is broken. I heard that the protein might have been broken which was observed from the failure of energy minimization which ended in just 1 step. See the Web's breaking stories, chosen by people like you.